Kronn Hunter Mode : At the beginning of the game, shoot the first three STAAR team members you see with the first three bullets (don't reload or miss). If you did this right you'll enter Kronn Hunter mode. In this mode, you are a mercenary from the Kronn hierarchy sent to sterilize Area 51 of the Kronn rebels. You will notice that the grenades, bullets, shotgun shells and machine gun bullets have all taken on a Kronn form.
Egg Cellent : On the forklift ride shoot all the barrels before and after the ride. There will be a partially hidden barrel you will have to shoot to the left of the forklift. This will lead you to 'egg cellent' where you shoot eggs and baby aliens.
Chow Palace : After your first progress report in Area 51, where it tells you your percentage and things like that, you will see a wall lined with windows. Shoot all the windows across the entire wall and you will be in the power up room, where you can see aliens attacking women and power-ups all over the screen.
Secret Area Before Final Boss : Right before you fight the Final Boss when you are outside, you will go to an area with zombies throwing barrels. Shoot all the barrels that are not thrown and you will go to a secret area filled with power ups.
Head Quarters : To see the alien restroom, you must shoot three blue lights that appear in the corners of the screen. At the beginning of the game, when you enter the building, shoot the first blue light in the upper left-hand corner of the screen. At the conclusion of level 1, while the screen is spinning, shoot the remaining two blue lights in the upper right-hand corner of the screen.
Secret Level : In the office building, you will go into a series of 2 or 3 doors with nameplates on all of them, shoot them all and then you will go into a secret room with power ups and an alien girl at the bottom.
X Marks The Spot : On the helicopter ride, shoot all of the boxes with flames on them. If done correctly, you will be sent into 'X Marks The Spot', which is a room where you keep breaking the glass on a wall with your guns to reveal a picture of a female police-person lying there in a very inviting position.
Spider Splat : In the level Computer Room Lockdown (where you can shoot the 13 computer terminal screens at the beginning of the level to get to the secret room). When the camera pans to the third scene, with the fire extinguishers and the staircase is in front of you, I'm not sure exactly what must be done, but if you shoot enough stuff you'll get access to a secret room called 'Spider Splat' where you have to shoot spiders that drop from the ceiling and save a woman.